Starting phenix.real_space_refine
on Fri Aug 22 17:21:52 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8unm_42409/08_2025/8unm_42409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unm_42409/08_2025/8unm_42409.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unm_42409/08_2025/8unm_42409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unm_42409/08_2025/8unm_42409.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unm_42409/08_2025/8unm_42409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unm_42409/08_2025/8unm_42409.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      38      5.16       5
     C    4128      2.51       5
     N    1110      2.21       5
     O    1136      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6415
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1641
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 224, 1629
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 5, 'TRANS': 218}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 242
          Unresolved non-hydrogen angles: 292
          Unresolved non-hydrogen dihedrals: 194
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'GLU:plan': 16, 'ASP:plan': 10, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 157
      Conformer: "B"
        Number of residues, atoms: 224, 1629
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 5, 'TRANS': 218}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 242
          Unresolved non-hydrogen angles: 292
          Unresolved non-hydrogen dihedrals: 194
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'GLU:plan': 16, 'ASP:plan': 10, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 157
          bond proxies already assigned to first conformer: 1647
    Chain: "B"
      Number of atoms: 2359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2359
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 206
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 6, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 14}
          Unresolved non-hydrogen planarities: 132
    Chain: "G"
      Number of atoms: 312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 312
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 2056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2056
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 7, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 247
          Unresolved non-hydrogen angles: 307
          Unresolved non-hydrogen dihedrals: 201
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLU:plan': 11, 'TRP:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 145
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 1.93, per 1000 atoms: 0.30
  Number of scatterers: 6415
  At special positions: 0
  Unit cell: (81.5638, 131.89, 97.1824, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       3     15.00
     O    1136      8.00
     N    1110      7.00
     C    4128      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 444.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      48.0% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 4.020A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 4.016A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.730A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.837A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 333 through 350
      removed outlier: 3.981A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 9 through 26
      removed outlier: 3.767A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.575A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 13 through 24
      removed outlier: 3.520A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.582A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.555A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.309A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 4.066A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.899A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.580A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.613A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.843A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 3.893A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.392A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.617A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 321
    Processing helix  chain 'R' and resid 322 through 327
      removed outlier: 3.600A  pdb=" N   CYS R 327 " --> pdb=" O   PRO R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 3.582A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.388A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   VAL A 287 " --> pdb=" O  ATYR A 360 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.716A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.048A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.070A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.150A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.830A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.700A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.836A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    984 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.76 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1281
        1.33 -     1.45: 1654
        1.45 -     1.57: 3567
        1.57 -     1.69: 5
        1.69 -     1.81: 50
  Bond restraints: 6557
  Sorted by residual:
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.479 -0.089 2.00e-02 2.50e+03 1.97e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.463 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" N   ASP A 310 "
       pdb=" CA  ASP A 310 "
    ideal  model  delta    sigma   weight residual
    1.459  1.423  0.036 1.20e-02 6.94e+03 9.01e+00
  bond pdb=" CA  ILE A 308 "
       pdb=" C   ILE A 308 "
    ideal  model  delta    sigma   weight residual
    1.522  1.478  0.044 1.50e-02 4.44e+03 8.73e+00
  bond pdb=" CA  GLU A 309 "
       pdb=" C   GLU A 309 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.037 1.30e-02 5.92e+03 7.88e+00
  ... (remaining 6552 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 8843
        2.11 -     4.22: 111
        4.22 -     6.33: 24
        6.33 -     8.43: 3
        8.43 -    10.54: 3
  Bond angle restraints: 8984
  Sorted by residual:
  angle pdb=" N   ASP A 323 "
        pdb=" CA  ASP A 323 "
        pdb=" C   ASP A 323 "
      ideal   model   delta    sigma   weight residual
     111.36  117.97   -6.61 1.09e+00 8.42e-01 3.67e+01
  angle pdb=" N   ALA A 324 "
        pdb=" CA  ALA A 324 "
        pdb=" C   ALA A 324 "
      ideal   model   delta    sigma   weight residual
     110.23  116.88   -6.65 1.45e+00 4.76e-01 2.10e+01
  angle pdb=" C   VAL R  34 "
        pdb=" CA  VAL R  34 "
        pdb=" CB  VAL R  34 "
      ideal   model   delta    sigma   weight residual
     111.97  106.54    5.43 1.28e+00 6.10e-01 1.80e+01
  angle pdb=" N   MET A  60 "
        pdb=" CA  MET A  60 "
        pdb=" C   MET A  60 "
      ideal   model   delta    sigma   weight residual
     111.28  107.13    4.15 1.09e+00 8.42e-01 1.45e+01
  angle pdb=" N   LYS A  58 "
        pdb=" CA  LYS A  58 "
        pdb=" C   LYS A  58 "
      ideal   model   delta    sigma   weight residual
     111.36  115.47   -4.11 1.09e+00 8.42e-01 1.42e+01
  ... (remaining 8979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.43: 3692
       31.43 -    62.85: 64
       62.85 -    94.28: 3
       94.28 -   125.71: 2
      125.71 -   157.13: 4
  Dihedral angle restraints: 3765
    sinusoidal: 1168
      harmonic: 2597
  Sorted by residual:
  dihedral pdb=" C4' GTP A 401 "
           pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  103.74  157.13     1      2.00e+01 2.50e-03 4.61e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  143.91  147.17     1      2.00e+01 2.50e-03 4.42e+01
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88   56.92 -142.80     1      2.00e+01 2.50e-03 4.31e+01
  ... (remaining 3762 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 754
       0.038 -    0.075: 223
       0.075 -    0.113: 85
       0.113 -    0.150: 14
       0.150 -    0.188: 4
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  TYR A 311 "
            pdb=" N   TYR A 311 "
            pdb=" C   TYR A 311 "
            pdb=" CB  TYR A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CA  ALA A 324 "
            pdb=" N   ALA A 324 "
            pdb=" C   ALA A 324 "
            pdb=" CB  ALA A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.32    0.17 2.00e-01 2.50e+01 6.90e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 1125
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 325 "   -0.046 5.00e-02 4.00e+02   6.98e-02 7.80e+00
        pdb=" N   PRO A 326 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 326 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 326 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 329 "   -0.039 5.00e-02 4.00e+02   5.94e-02 5.65e+00
        pdb=" N   PRO R 330 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO R 330 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 330 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO R 211 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1122 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 733
        2.75 -     3.28: 6015
        3.28 -     3.82: 10014
        3.82 -     4.36: 10783
        4.36 -     4.90: 20309
  Nonbonded interactions: 47854
  Sorted by model distance:
  nonbonded pdb=" O   THR A 325 "
            pdb=" OH  TYR A 339 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLN A 267 "
            pdb=" OD1 ASN A 271 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" NE2 HIS A 220 "
            pdb=" CZ  PHE A 222 "
     model   vdw
     2.410 3.420
  ... (remaining 47849 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.400
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   6558  Z= 0.253
  Angle     :  0.639  10.542   8986  Z= 0.369
  Chirality :  0.042   0.188   1080
  Planarity :  0.004   0.070   1125
  Dihedral  : 13.954 157.134   2074
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.29), residues: 872
  helix:  2.26 (0.27), residues: 378
  sheet:  0.16 (0.41), residues: 172
  loop : -1.01 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 356 
 TYR   0.026   0.001   TYR B  59 
 PHE   0.013   0.001   PHE B 235 
 TRP   0.007   0.001   TRP R  99 
 HIS   0.012   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6557)
  covalent geometry    : angle       0.63920 ( 8984)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.91435 (    2)
  hydrogen bonds       : bond        0.16714 (  338)
  hydrogen bonds       : angle       5.83943 (  984)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0683
  time to fit residues: 9.0588
Evaluate side-chains
  68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.116589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.090563 restraints weight = 37341.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 5.09
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6558  Z= 0.161
  Angle     :  0.510   6.676   8986  Z= 0.280
  Chirality :  0.043   0.156   1080
  Planarity :  0.004   0.052   1125
  Dihedral  : 10.439 152.604    969
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  8.66 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.29), residues: 872
  helix:  2.15 (0.27), residues: 392
  sheet:  0.10 (0.40), residues: 174
  loop : -0.89 (0.31), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 356 
 TYR   0.028   0.001   TYR B  59 
 PHE   0.010   0.001   PHE A 376 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.018   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6557)
  covalent geometry    : angle       0.50979 ( 8984)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       0.80956 (    2)
  hydrogen bonds       : bond        0.04991 (  338)
  hydrogen bonds       : angle       4.43386 (  984)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 77
  average time/residue: 0.0787
  time to fit residues: 8.4648
Evaluate side-chains
  73 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  128 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 67 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.118707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.092447 restraints weight = 39978.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 5.15
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6558  Z= 0.105
  Angle     :  0.457   7.460   8986  Z= 0.244
  Chirality :  0.041   0.154   1080
  Planarity :  0.004   0.048   1125
  Dihedral  :  9.625 152.187    969
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.89 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.29), residues: 872
  helix:  2.43 (0.27), residues: 388
  sheet:  0.31 (0.41), residues: 174
  loop : -0.82 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.011   0.001   PHE R  61 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.011   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6557)
  covalent geometry    : angle       0.45677 ( 8984)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.76104 (    2)
  hydrogen bonds       : bond        0.03806 (  338)
  hydrogen bonds       : angle       3.90878 (  984)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.7830 (tpp) cc_final: 0.7566 (tpp)
  outliers start: 6
  outliers final: 3
  residues processed: 82
  average time/residue: 0.0681
  time to fit residues: 7.9581
Evaluate side-chains
  76 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain R residue   77 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0980
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.116580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.090265 restraints weight = 31288.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 4.63
r_work: 0.2957 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6558  Z= 0.141
  Angle     :  0.485   7.013   8986  Z= 0.259
  Chirality :  0.042   0.159   1080
  Planarity :  0.004   0.045   1125
  Dihedral  :  9.435 153.545    969
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.95 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.29), residues: 872
  helix:  2.34 (0.27), residues: 393
  sheet:  0.18 (0.40), residues: 174
  loop : -0.82 (0.31), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 342 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.011   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6557)
  covalent geometry    : angle       0.48484 ( 8984)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.72013 (    2)
  hydrogen bonds       : bond        0.04417 (  338)
  hydrogen bonds       : angle       3.91465 (  984)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8017 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0600
  time to fit residues: 7.4210
Evaluate side-chains
  81 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   chunk 73 optimal weight:    0.0670
   chunk 83 optimal weight:    0.0050
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.3742

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.120888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.094296 restraints weight = 43368.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 5.62
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6558  Z= 0.088
  Angle     :  0.440   7.300   8986  Z= 0.231
  Chirality :  0.040   0.152   1080
  Planarity :  0.003   0.043   1125
  Dihedral  :  8.919 153.410    969
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.01 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.29), residues: 872
  helix:  2.66 (0.27), residues: 383
  sheet:  0.36 (0.40), residues: 173
  loop : -0.81 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R  61 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 6557)
  covalent geometry    : angle       0.43982 ( 8984)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.73243 (    2)
  hydrogen bonds       : bond        0.03134 (  338)
  hydrogen bonds       : angle       3.59969 (  984)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: B  143 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9116 (p)
REVERT: B  234 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8034 (m-80)
REVERT: B  259 GLN cc_start: 0.8666 (pm20) cc_final: 0.7654 (pm20)
  outliers start: 8
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0675
  time to fit residues: 9.3336
Evaluate side-chains
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   77 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 70 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0370
   chunk 36 optimal weight:    0.2980
   chunk 13 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0060
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.2474

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.122372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.095596 restraints weight = 35016.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 5.00
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6558  Z= 0.082
  Angle     :  0.432   7.059   8986  Z= 0.226
  Chirality :  0.040   0.174   1080
  Planarity :  0.003   0.046   1125
  Dihedral  :  8.511 147.595    969
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.43 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.29), residues: 872
  helix:  2.75 (0.27), residues: 384
  sheet:  0.34 (0.39), residues: 180
  loop : -0.70 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.018   0.001   PHE R  61 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00159 ( 6557)
  covalent geometry    : angle       0.43158 ( 8984)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.66208 (    2)
  hydrogen bonds       : bond        0.02867 (  338)
  hydrogen bonds       : angle       3.43858 (  984)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 ASN cc_start: 0.8773 (m110) cc_final: 0.8540 (m-40)
REVERT: B  143 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.9110 (p)
REVERT: B  234 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8137 (m-80)
REVERT: B  259 GLN cc_start: 0.8689 (pm20) cc_final: 0.7671 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 103
  average time/residue: 0.0860
  time to fit residues: 11.8302
Evaluate side-chains
  91 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   77 CYS
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 322 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.092260 restraints weight = 30629.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 4.70
r_work: 0.2989 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2982
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6558  Z= 0.118
  Angle     :  0.485  11.877   8986  Z= 0.249
  Chirality :  0.041   0.170   1080
  Planarity :  0.003   0.050   1125
  Dihedral  :  8.649 146.822    969
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.25 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.29), residues: 872
  helix:  2.75 (0.27), residues: 384
  sheet:  0.39 (0.40), residues: 174
  loop : -0.80 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.018   0.001   PHE A 222 
 TRP   0.005   0.001   TRP B  63 
 HIS   0.013   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6557)
  covalent geometry    : angle       0.48453 ( 8984)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.59683 (    2)
  hydrogen bonds       : bond        0.03771 (  338)
  hydrogen bonds       : angle       3.53595 (  984)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: B  143 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9094 (p)
REVERT: B  234 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8213 (m-80)
REVERT: B  259 GLN cc_start: 0.8952 (pm20) cc_final: 0.8295 (pm20)
  outliers start: 13
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0676
  time to fit residues: 8.7814
Evaluate side-chains
  95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   77 CYS
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0020
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.4546

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.121170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.094395 restraints weight = 33861.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 5.00
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6558  Z= 0.088
  Angle     :  0.453   9.624   8986  Z= 0.233
  Chirality :  0.040   0.179   1080
  Planarity :  0.003   0.058   1125
  Dihedral  :  8.614 145.204    969
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.84 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.29), residues: 872
  helix:  2.76 (0.27), residues: 384
  sheet:  0.56 (0.40), residues: 173
  loop : -0.77 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 342 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.017   0.001   PHE A 222 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 ( 6557)
  covalent geometry    : angle       0.45261 ( 8984)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.66446 (    2)
  hydrogen bonds       : bond        0.03047 (  338)
  hydrogen bonds       : angle       3.41896 (  984)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8341 (mtt) cc_final: 0.8100 (mtt)
REVERT: B   59 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: B  143 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9042 (p)
REVERT: B  234 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8245 (m-80)
REVERT: B  259 GLN cc_start: 0.8692 (pm20) cc_final: 0.8038 (pm20)
  outliers start: 12
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0713
  time to fit residues: 9.4041
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0980
   chunk 48 optimal weight:    0.1980
   chunk 18 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.120677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.093738 restraints weight = 37073.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 5.12
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6558  Z= 0.092
  Angle     :  0.464   9.982   8986  Z= 0.235
  Chirality :  0.040   0.186   1080
  Planarity :  0.003   0.062   1125
  Dihedral  :  8.705 158.420    969
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.84 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.29), residues: 872
  helix:  2.76 (0.27), residues: 384
  sheet:  0.59 (0.41), residues: 173
  loop : -0.76 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.018   0.001   PHE A 222 
 TRP   0.005   0.001   TRP B 297 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 6557)
  covalent geometry    : angle       0.46371 ( 8984)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.64689 (    2)
  hydrogen bonds       : bond        0.03199 (  338)
  hydrogen bonds       : angle       3.40360 (  984)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8254 (mtt) cc_final: 0.8017 (mtt)
REVERT: B   59 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7640 (m-80)
REVERT: B  143 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9029 (p)
REVERT: B  234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8236 (m-80)
REVERT: B  259 GLN cc_start: 0.8698 (pm20) cc_final: 0.8029 (pm20)
  outliers start: 12
  outliers final: 9
  residues processed: 95
  average time/residue: 0.0835
  time to fit residues: 10.5601
Evaluate side-chains
  99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0980
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.118695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.091595 restraints weight = 30226.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 4.58
r_work: 0.2988 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6558  Z= 0.115
  Angle     :  0.477   9.614   8986  Z= 0.246
  Chirality :  0.041   0.183   1080
  Planarity :  0.003   0.058   1125
  Dihedral  :  8.987 176.890    969
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.19 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.29), residues: 872
  helix:  2.71 (0.27), residues: 384
  sheet:  0.46 (0.40), residues: 174
  loop : -0.82 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.006   0.001   TYR A 339 
 PHE   0.015   0.001   PHE R  61 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.013   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6557)
  covalent geometry    : angle       0.47682 ( 8984)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.64093 (    2)
  hydrogen bonds       : bond        0.03738 (  338)
  hydrogen bonds       : angle       3.50575 (  984)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8334 (mtt) cc_final: 0.8113 (mtt)
REVERT: B   59 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8360 (m-80)
REVERT: B  143 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9045 (p)
REVERT: B  234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8223 (m-80)
REVERT: B  259 GLN cc_start: 0.8948 (pm20) cc_final: 0.8295 (pm20)
  outliers start: 12
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0799
  time to fit residues: 10.0039
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.091270 restraints weight = 39139.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 5.29
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6558  Z= 0.112
  Angle     :  0.481   9.678   8986  Z= 0.246
  Chirality :  0.041   0.180   1080
  Planarity :  0.003   0.060   1125
  Dihedral  :  8.777 170.322    969
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.19 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.29), residues: 872
  helix:  2.68 (0.27), residues: 384
  sheet:  0.53 (0.40), residues: 172
  loop : -0.85 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.017   0.001   PHE R  61 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.013   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6557)
  covalent geometry    : angle       0.48099 ( 8984)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.71610 (    2)
  hydrogen bonds       : bond        0.03704 (  338)
  hydrogen bonds       : angle       3.51544 (  984)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1530.86 seconds
wall clock time: 26 minutes 51.87 seconds (1611.87 seconds total)